区分分子钟的趋同进化和破坏
Distinguishing between convergent evolution and violation of the molecular clock
摘要：
我们给出了收敛-发散模型的非技术性介绍，这是一种新的系统发育数据建模方法，允许物种形成后的通常发散，但也允许物种收敛，即随着时间的推移变得更加相似。通过详细研究$3$ -分类单元的情况，我们说明了遗传学家由于进化是树型的强假设而不必考虑模型中的结构参数，这在某种意义上是“被宠坏了”。我们发现，并不总是有很好的统计理由，更一般的收敛-发散模型，更喜欢通常的类树模型。具体来说，我们发现许多$3$ -分类单元数据集可以同样很好地解释假设违反分子时钟由于沿不同的边缘的进化速率的变化，或保持一个恒定的进化速率的假设，而是假设进化不是一个纯粹的发散过程。鉴于有大量证据表明进化并不是严格意义上的树状进化，我们的讨论说明，作为遗传学家，我们经常需要清楚地思考我们所使用的模型的结构形式。
英文摘要：
We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of species post speciation but also allows for species to converge, i.e. become more similar over time. By examining the $3$-taxon case in some detail we illustrate that phylogeneticists have been "spoiled" in the sense of not having to think about the structural parameters in their models by virtue of the strong assumption that evolution is treelike. We show that there are not always good statistical reasons to prefer the usual class of treelike models over more general convergence-divergence models. Specifically we show many $3$-taxon datasets can be equally well explained by supposing violation of the molecular clock due to change in the rate of evolution along different edges, or by keeping the assumption of a constant rate of evolution but instead assuming that evolution is not a purely divergent process. Given the abundance of evidence that evolution is not strictly treelike, our discussion is an illustration that as phylogeneticists we often need to think clearly about the structural form of the models we use.
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